A novel in-line surface-induced dissociation (
SID) device was designed and implemented in a commercial QTOF instrument (Waters/Micromass QTOF II). This new setup allows efficient
SID for a broad range of molecules. It also allows direct comparison with conventional collision-induced dissociation (CID) on the same instrument, taking advantage of the characteristics of QTOF instrumentation, including extended mass range, improved sensitivity, and better resolution compared with quadrupole analyzers and ion traps. Various
peptides and a noncovalent
protein complex have been electrosprayed and analyzed with the new
SID setup. Here we present
SID of
leucine enkephalin,
fibrinopeptide A,
melittin,
insulin chain-B, and a noncovalent
protein complex from wheat,
heat shock protein 16.9. The
SID spectra were also compared to CID spectra. With the
SID setup installed, ion transmission proved to be efficient.
SID fragmentation patterns of
peptides are, in general, similar to CID, with differences in the relative intensities of some peaks such as immonium
ions, backbone cleavage b- versus y-type
ions, and y- versus y-NH3
ions, suggesting enhanced accessibility to high-energy/secondary fragmentation channels with
SID. Furthermore, these results demonstrate that the in-line
SID setup is a valid substitute for CID, with potential advantages for activation of singly/multiply charged
peptides and larger species such as noncovalent
protein complexes.